org.broadinstitute.hellbender.tools.spark.sv.discovery.inference

Class SegmentedCpxVariantSimpleVariantExtractor

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor

All Implemented Interfaces:

java.io.Serializable

public abstract class SegmentedCpxVariantSimpleVariantExtractor
extends java.lang.Object
implements java.io.Serializable

For extracting simple variants from input GATK-SV complex variants. Some explanation on several concepts:

Anchor ref base: anchor base is defined per-VCF spec (see 1.4.1#REF version 4.2), that is, for DEL and INS variants the reference base at the position pointed to by POS, basically: for DEL, the reference bases immediately following POS are deleted (up to and including the END base), for INS, the sequence annotated in INSSEQ are inserted immediately after POS.

"Fat" insertion: they exist because sometimes we have micro deletions surrounding the insertion breakpoint, so here the strategy is to report them as "fat", i.e. the anchor base and deleted bases are reported in REF; they are fat in the sense that compared to simple insertions where a single anchor ref base is necessary

It is also assumed that POS and END of the input complex VariantContext are the boundaries of the bases where REF and ALT allele share similarity, in other words, immediately after POS and before END is where the REF and ALT allele differ, and the two path merges at POS/END.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants

Constructor Summary

Constructors

Constructor and Description
SegmentedCpxVariantSimpleVariantExtractor()

Method Summary

Modifier and Type	Method and Description
static SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants	extract(org.apache.spark.api.java.JavaRDD<htsjdk.variant.variantcontext.VariantContext> complexVariants, SvDiscoveryInputMetaData svDiscoveryInputMetaData, org.apache.spark.api.java.JavaRDD<GATKRead> assemblyRawAlignments)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SegmentedCpxVariantSimpleVariantExtractor

public SegmentedCpxVariantSimpleVariantExtractor()

Method Detail

extract

public static SegmentedCpxVariantSimpleVariantExtractor.ExtractedSimpleVariants extract(org.apache.spark.api.java.JavaRDD<htsjdk.variant.variantcontext.VariantContext> complexVariants,
                                                                                        SvDiscoveryInputMetaData svDiscoveryInputMetaData,
                                                                                        org.apache.spark.api.java.JavaRDD<GATKRead> assemblyRawAlignments)